3TOZ | pdb_00003toz

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3toza2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
A	d3toza1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
B	d3tozb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
B	d3tozb1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
C	d3tozc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
C	d3tozc1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
D	d3tozd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
D	d3tozd1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
E	d3toze2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
E	d3toze1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
F	d3tozf2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
F	d3tozf1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
G	d3tozg2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
G	d3tozg1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
H	d3tozh2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)
H	d3tozh1	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	automated matches	automated matches	(Listeria monocytogenes EGD-e ) [TaxId: 169963 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	MtdA-like	8074726	3000046	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ion_trans_2	e3tozA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
B	Ion_trans_2	e3tozB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
C	Ion_trans_2	e3tozC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
D	Ion_trans_2	e3tozD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
E	Ion_trans_2	e3tozE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
F	Ion_trans_2	e3tozF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
G	Ion_trans_2	e3tozG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)
H	Ion_trans_2	e3tozH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ion_trans_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF08501	Shikimate dehydrogenase substrate binding domain (Shikimate_dh_N)	Shikimate dehydrogenase substrate binding domain	This domain is the substrate binding domain of shikimate dehydrogenase [1].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF18317	Shikimate 5'-dehydrogenase C-terminal domain (SDH_C)	Shikimate 5'-dehydrogenase C-terminal domain	This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found j ...	This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found just after the C-terminal domain (Pfam:PF01488) which is responsible for NADP binding [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Shikimate dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors shikimate 3-dehydrogenase (NADP+) activity catalytic activity binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process shikimate metabolic process monocarboxylic acid metabolic process organic acid metabolic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process shikimate metabolic process monocarboxylic acid metabolic process organic acid metabolic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process chorismate metabolic process chorismate biosynthetic process dicarboxylic acid biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022893	Shikimate dehydrogenase family	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011342	Shikimate dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR041121	SDH, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013708	Shikimate dehydrogenase substrate binding, N-terminal	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.